Lab In Snow: Creating Massive Genome Sequences In Glaciers And Ice Caps

Lab In Snow: Creating Massive Genome Sequences In Glaciers And Ice Caps

Courtesy Oxford Nanopore Tech.

To understand more about life and this world, opportunities are hidden in nature, new knowledge presents itself to be taken up for the mankind, new ways to unlock knowledge of life the genomes of living organisms are of key importance. The genome is composed of all the knowledge of life containing all information which can help in revealing many issues of life. For achieving these targets getting sequences of genome is important. Since the completion of Human Genome Project the sequencing techniques have been gradually improved day by day. But one of the major constrains in this journey is the detailed preparation of genomic libraries, transportation of these sample labs from one city to another and in some cases other country or even another continent. These sorts of delays could cost a lot in a longer view; in sort of genomic degradation, delayed results and some time loss of nascent species. In this moment of anxiety the answer came from Oxford University in form of their all new portable nano-pore sequencers “The MinION” (See:https://crisprpedia.blogspot.com/2018/10/minion-ultimate-future-of-genome.html). These sequencers have produced viable results in labs and following initial success the sequencer are now being tested in some extreme conditions. This post is focused on some such beautiful journey of creating massive sequencing in extreme conditions.

Journey to the Ice of Iceland:

Dr. Sarah Johnson from the Georgetown University went on to employ nano-pore sequencers to the remote ice caps of Iceland. She explained her journey to be remarkable, easy, fun, learning and adventurous. She greatly admired the level of easiness provided by the nanopore sequencers as multiple samples from different soils, lakes, and glaciers were collected with the corresponding genomic libraries prepared within a day and ready to be sequenced. They also observed a very negligible level of contamination during genomic library preparation prepared following protocols given by the Oxford Nanopore and using corresponding DNA kits. The key benefit of nanopore sequence was its swiftness and rapid result output with first results available in approx 30 mins. Dr. Sarah Johnson and her team greatly admired the minion sequencer and corresponding analysis tools as the enabled covering a large area in small time with a vast variety of samples analysed in a limited time period.

Courtesy Johnson  Biosignatures Labs.

Exploring glacier diversity of Greenland:

Conducting massive sequencing research in remote glaciers is always a great challenge. Dr. Arwyn Edward and his team worked on massive Russell glaciers of Greenland. Ice caps and glaciers command a beautiful diversity of life ready to be explored but often face a serious constrain in from of subzero temperature which makes the overall operation difficult to carried out. Dr. Arwyn and his team hoped to break this stereotype as the conducted massive meta-genomic sequences in Greenland and explored new microbial communities. The operation was carried out using the portable nano-pore sequencers the MinION. Meta-genomic libraries were prepared using corresponding extraction kits and fed to MinION for sequencing. In this way massive metagenomic sequences were carried out in ice glaciers in real time.

Conclusion:

Glaciers and ice caps covers a significant region of earth’s surface with an entire continent made up of ice and large regions in poles covered with ice, these places are usually having extreme weather conditions, subzero temperatures, long dark days, these conditions are un-conducive for human life sustainability so why is it still important for us to explore microbial communities and analyse all this data?? Answer to this question lie in the fact that climate change and rise in global temperatures is causing rapid melt and loss of ice sheets and their addition in mainstream water supply, along with these ice sheets corresponding microbial communities will become a part of water supplies as well. In time metagenomic sequences will help in timely identification of threat either the microbes are harmful or not and what steps should be taken to counter the threat. Recent reports already explains the havoc climate change is bringing with it as the permafrost melt releases some deadly pathogens back in environment after centuries of dormancy, real time sequencing could be helpful for countering this issue as well as real time sequencing will enable in time confirmation and marking geographical distribution pattern of such deadly pathogens and strategies to contain the plague.

Source: Oxford nano-pore, Johnson Biosignatures Lab, Psychropaths

CRISPR: A Technology Breaking Records

CRISPR: A Technology Breaking Records

The world around us, the world in which we live, the world in which we reside, the world in which we thrive is greatly affected by science and technology. Since the dawn of evolution every scientific discovery has one key objective the betterment of mankind to make life of humans better. The beginning of 21^st century came with a promise to be a century of ultimate evolution and scientific marvels and among those marvels is the renowned Genome Editing technology the “CRISPR”. Since its introduction in late 2010’s the tech has completely revolutionized every field of science from bio medicines to pharmaceuticals to agriculture. The technology is a promising tech owing to its great impact and positive results. Apart from the ethical dilemma involving human gene editing one of the key targets that remain insight with this great tech in hand is to manage and find cure for various genetic disorders. This aim just got a new boost as the CRISPR broke another record.

Breaking the Record:

An essential focus with the CRISPR technology is to achieve multiplex editing and dealing with junk DNA. George church a globally renowned geneticist alongside his team previously performed an experiment involving removal of 62 copies of retroviral DNA lurking around the pig genome the target was to remove viral DNA avoid chances of infection by viruses and making smooth transition for pig-human organ transplant possible. This was previously the best results and probably highest number of the edits performed in a single gene editing experiment. A recent effort by the same scientific team headed by Dr. Church and including their associates Oscar Castanon and Cory Smith includes mass scale alteration of genome and its post edit viability estimation. The team have just submitted their findings which states they have successfully altered the genome at 13200 locations and the cell survived after the experiment. One of the major constraints of CRISPR genome editing is to ensure that the experiment is feasible and cell survives, live and able to reproduce after the experiment. In this study the team target a large segment of DNA called the LINE-1—which is a large transposable element able to shift itself along the genome and is reportedly about 17% of the total human genome. The LINE1 has been reported to cause some devastating disease including haemophilia, colon cancer and many more, which indicates a dire need for solution but in the mean time dealing with it is a huge challenge as it consists of such a large portion of our DNA. But despite of all these hurdles the team achieved a milestone they have altered the LINE1 from about 13000 spots with an all new version of the CRISPR/CAS called the base editor and the cell successfully survived in post experimental evaluations.

George Church(Left) Oscar Castanon and Cory Smith (Right)

Prior to this research many renowned scientists across the globe have attempted to deal with the LINE1 using the CRISPR but none was able to find some effective results. For instance in 2016 Dr. Geoff Faulkner from the University of Queensland in Australia worked with CRISPR as he attempted to knock out LINE from about 500 mice embryos but the final results showed none of the embryos could survive mass scale editing. After knowing the results from Dr. Church’s team he himself praised this new approach and said:

“They found a way to do the experiment without causing gross genome-wide instability”

—Dr.Geoff Faulkner

In a closely related study in 2017 another Australian Scientist Dr. Paul Thomas created massive edits in Y chromosome of mice and pushed it out of the frame the results of the study shows great potential for the tech to cure certain genetic disorders like down’s syndrome.

Conclusion:

With every single day passing on human race is facing new and new challenges which is met by an equally high efforts from mankind to deal with these issues. These new results shows how widely can the genome editing be used to cure not one but multiple ailments and its ultimate influence as one of the deciding factors for the better survival of mankind.